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Seed dispersal distances (SDD) critically influence the survival of seedlings, spatial patterns of genetic diversity within plant populations and gene flow among plant populations. In tropical forests, a large percentage of seeds is dispersed by animals, and their foraging behaviour and movement patterns determine SDD. Direct observations of seed dispersal events by animals in natural plant populations are mostly constrained by the high mobility and low visibility of their vectors. Therefore, diverse alternative methods are used to estimate SDD, but direct comparisons of these approaches within the same seed dispersal system are mostly missing. In this study, we take advantage of two plant species with different life history traits, Leonia cymosa and Parkia panurensis that are exclusively dispersed by two tamarin species, Saguinus mystax and Leontocebus nigrifrons (Callitrichidae) at our study site in the Peruvian Amazon. We compare SDD estimates obtained from direct observations, genetic identification of mother plants from seed coats, parentage analysis of seedlings, and modelling approaches, including the combination of movement data and gut passage times and individual-based modelling. We detect differences between SDD estimates that can be linked to the processes relevant at different phases of the seed dispersal loop covered by the respective approaches. Despite these differences, SDD estimates for P. panurensis are consistently lower than for L. cymosa which is likely related to differences in fruit characteristics and fruit abundance, factors that influence gut passage time, foraging behaviour and movement patterns of the tamarins. Our comparisons allow setting SDD estimates from studies using different methodological approaches into the seed dispersal loop context, thus improving comparability of methodologically different studies and method applicability.